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<center><a href='http://biocodecommons.org/'><img height=100 src='logos/biocodecommonsTrans.png' border =0></a></center>
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<center><i><strong>Resources for genomic observations from collection to analysis and publication</strong></i></center>
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<center><b><a href="http://biocodecommons.blogspot.com/">Biocode Commons Blog</a></b></center>

<p>The space between standards and software, standards and other standards, and between software and other software, is what we are calling the "commons". Hence, the "Biocode Commons" specifically addresses the gap present in the biodiversity genomics community between collections based data (commonly museum specimens and tissues) and the sequence based data sets. </p>

<p><b>Biological Collections Ontology (BCO) Paper published in <a href='http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0089606'>PloSONE</a></b>  
<p>The BCO represents an important step forward in our thinking about how to represent genomics and biodiversity data

<p><b>Tools and Resources</b></p>

<!--The Biocode Commons facilitates the integration and re-use of tools, adopting web-services, shared code, and project to project communications.The following tools are official contributions to the Biocode Commons core set of tools.-->

<dir><a href='http://biosharing.org/'>Biosharing</a> works to map the landscape of community developed standards in the life sciences, broadly covering biological, natural and biomedical sciences.</dir>

<dir><a href='http://isa-tools.org/'>ISA Tools</a> helps you to provide a rich description of your experimental metadata.</dir>

<dir><a href='http://biscicol.org/bcid'>BCIDs</a> (Biocode Commons Identifiers) are used for tagging and tracking physical samples of biological material.</dir>

<dir>Biocode <a href='http://code.google.com/p/biocode-fims'>FIMS</a> and <a href='http://software.mooreabiocode.org'>LIMS</a> are tools for tracking samples from the field field through the lab (FIMS/LIMS stands for Field/Laboratory Information Management System).</dir>

<dir>The <a href='https://code.google.com/p/bco/'>Biological Collections Ontology</a> is an effort to model genomic biodiversity and related samples and processes, building off of the <a href='http://www.ifomis.org/bfo'>BFO</a>, <a href='http://obi-ontology.org/page/Main_Page'>OBI</a>, <a href='http://gensc.org/projects/mixs-gsc-project/'>MIxS</a>, and <a href='http://rs.tdwg.org/dwc/terms/'>Darwin Core</a>.</dir>

<p><b>Workshops and Hackathons</b></p>

Periodic workshops and hackathons, sponsored by Biocode Commons, in conjunction withthe RCN4GSC, I3BEager, and BiSciCol NSF grants.
  <dir>Genomic Biodiversity Working Group / Biocode Commons Hackathon at the <a href='http://gensc.org/uncategorized/gsc-16-oxford/'>GSC16 meeting</a>, Oxord, UK (April 1-2, 2014).  This hackathon will be focused on building components of the <a href='https://code.google.com/p/bco/'>Biological Collections Ontology</a> and creating a <a href='https://code.google.com/p/darwincore/issues/detail?id=167'>MaterialSample</a> Core using <a href='http://www.gbif.org/'>GBIF's</a> <a href='http://ipt.gbif.org/'>Integrated Publishing Toolkit</a>  -- Description Coming Soon.</dir>

  <dir>Biological Collections Ontology / Population and Community Ontology Coding Workshop at the University of Arizona (February, 2014) (Summary of this meeting is coming soon)</dir>

  <dir><a href="workshops/bioCollections/index.html">Biological Collections Ontology / Biocode Commons Hackathon, GSC14 (September, 2012)</a></dir>

  <dir><a href="workshops/3bi/3bi.html">Berkeley, BiSciCol, BigData, Identifiers, and VertNet (3Biv) (August, 2012)</a></dir>

  <dir><a href="https://docs.google.com/document/d/1QcOXPAt67c68L6qKfR-P51w08Hb0k03FjEO8PpkD8Jg/edit">Biocode Moorea Genomic Observatory Workshop (June, 2012)</a></dir>

  <dir><a href="workshops/sob.html">Semantics of Biodiversity Workshop at KU (May, 2012)</a></dir>

<p><b>Standards and Community</b></p>

<p>The Biocode Commons is working with the standards community to ensure clear vocabularies and useful ontologies for biological resources and related assets through periodic workshops and hackathons and the <a href='http://biosharing.org/'>BioSharing Network</a>. Links to the standards community are through the workings of the <a href='http://gensc.org/projects/biodiversity-genomics-working-group/'>Genomic Biodiversity Working Group</a> (partnering with <a href='http://gensc.org/'>GSC</a> and <a href='http://tdwg.org/'>TDWG</a>).  Biocode Commons is also collaborating on the development of the <a href='http://code.google.com/p/bco/'>Biological Collections Ontology (BCO)</a>, working generally to better integrate ontologies, vocabularies, and relevant standards that are related to BCO.</p>


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<b>A community of developers</b>
<br><i>Increasing communication between development teams working on biodiversity informatics, genomics, publication, and analysis through periodic workshops and hackathons.
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<b>Tools for Scientists</b>
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<i>Facilitating the integration and re-use of tools, adopting web-services, shared code, and project to project communications.</i>
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<b>Ecosystem of Standards</b>
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Working with the standards community to ensure clear vocabularies and useful ontologies for genomic resources.
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<a href='http://moore.org/'><img height=40 src='logos/moore_logo.jpg'></a>
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<a href='http://www.biomatters.com/'><img height=40 src='logos/geneious_logo.png'></a>
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<a href='http://www.tdwg.org/'><img height=40 src='logos/tdwg_logo.gif'></a>
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<a href='http://www.genomicobservatories.org/'><img src='logos/genomicobservatories.png' width="239" height=40></a>
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<b>Workshops and Hackathons</b>
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<li><a href="http://tinyurl.com/biocodeCommonsHackathon">Biocode Commons Hackathon at GSC14 (September, 2012)</a></li>
<li><a href="workshops/3bi/3bi.html">Berkeley, BiSciCol, BigData, Identifiers, and VertNet (3Biv) (August, 2012)</a></li>
<li><a href="https://docs.google.com/document/d/1QcOXPAt67c68L6qKfR-P51w08Hb0k03FjEO8PpkD8Jg/edit">Biocode Moorea Genomic Observatory Workshop (June, 2012)</a></li>
<li><a href="workshops/sob.html">Semantics of Biodiversity Workshop at KU (May, 2012)</a></li>
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<b>Tools Contributed to the Biocode Commons</b>
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<li><a href='http://biovalidator.sourceforge.net/'>bioValidator: Biocode FIMS</a></li>
<li><a href=' http://software.mooreabiocode.org/index.php?title=Main_Page'>LIMS: Geneious Genetic Resource Management</a></li>
<li><a href='http://www.isa-tools.org/'>Experimental descriptions: ISA tools</a>
<li><a href='http://biscicol.org/triplifier/'>The BiSciCol Triplifier (beta)</a>
<li><a href='http://nebc.nerc.ac.uk/tools/bio-linux/bio-linux-6.0'>bio-linux</a>
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<b>Standards Partners</b>
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<li><a href='http://gensc.org/gc_wiki/index.php/Main_Page'>GSC (Genomic Standards Consortium)</a></li>
<li><a href='www.tdwg.org'>TDWG (Biodiversity Information Standards)</a></li>
<li><a href='http://www.biosharing.org/standards_view'>BioSharing catalogue</a></li>
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